Variant report

Variant	rs6474732
Chromosome Location	chr9:12815091-12815092
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:12814029-12816382	IMR90	lung:	n/a	n/a
2	JUND	chr9:12813946-12815294	SK-N-SH	brain:	n/a	chr9:12814448-12814460 chr9:12814593-12814603 chr9:12814594-12814603 chr9:12814593-12814602 chr9:12814501-12814510 chr9:12814597-12814605 chr9:12814594-12814601 chr9:12814592-12814603
3	GATA3	chr9:12813852-12815101	SK-N-SH	brain:	n/a	chr9:12814878-12814885
4	MAX	chr9:12813971-12815192	Hela-S3	cervix:	n/a	chr9:12814672-12814682 chr9:12814420-12814429
5	POLR2A	chr9:12813949-12815102	MCF10A-Er-Src	breast:	n/a	n/a
6	PRDM1	chr9:12813966-12815093	Hela-S3	cervix:	n/a	chr9:12814952-12814966 chr9:12814594-12814603 chr9:12814593-12814602 chr9:12814952-12814965
7	KAP1	chr9:12813996-12815173	HEK293	kidney:	n/a	chr9:12814595-12814604 chr9:12814592-12814601
8	MXI1	chr9:12813414-12815225	SK-N-SH	brain:	n/a	n/a
9	EP300	chr9:12813738-12815502	SK-N-SH	brain:	n/a	chr9:12814418-12814432 chr9:12815249-12815263 chr9:12814594-12814603 chr9:12814543-12814557 chr9:12814499-12814508
10	TCF12	chr9:12814032-12815112	SK-N-SH	brain:	n/a	n/a
11	FOSL2	chr9:12813821-12815140	A549	lung:	n/a	chr9:12814448-12814460 chr9:12814593-12814603 chr9:12814594-12814603 chr9:12814593-12814602 chr9:12814501-12814510 chr9:12814597-12814605 chr9:12814594-12814601
12	TCF12	chr9:12813960-12815122	SK-N-SH	brain:	n/a	n/a
13	MAFK	chr9:12811989-12815225	Hela-S3	cervix:	n/a	chr9:12812902-12812917 chr9:12812907-12812916 chr9:12812907-12812917 chr9:12814594-12814604 chr9:12813705-12813720
14	TCF12	chr9:12813773-12815162	A549	lung:	n/a	n/a
15	POLR2A	chr9:12813976-12816199	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr9:12814051-12815185	HepG2	liver:	n/a	n/a
17	CEBPB	chr9:12813422-12815135	Hela-S3	cervix:	n/a	chr9:12814579-12814590
18	BCL3	chr9:12813964-12815230	A549	lung:	n/a	chr9:12814953-12814962
19	JUN	chr9:12814124-12815141	Hela-S3	cervix:	n/a	chr9:12814448-12814460 chr9:12814593-12814603 chr9:12814594-12814603 chr9:12814593-12814602 chr9:12814501-12814510 chr9:12814597-12814605 chr9:12814594-12814601
20	EP300	chr9:12813762-12815130	A549	lung:	n/a	chr9:12814418-12814432 chr9:12814594-12814603 chr9:12814543-12814557 chr9:12814499-12814508
21	SP1	chr9:12813890-12815168	HCT-116	colon:	n/a	n/a
22	GATA3	chr9:12813765-12815199	A549	lung:	n/a	chr9:12814878-12814885
23	SIN3AK20	chr9:12814237-12815136	MCF-7	breast:	n/a	n/a
24	CEBPB	chr9:12813976-12815149	HCT-116	colon:	n/a	chr9:12814579-12814590
25	MAX	chr9:12813825-12815094	A549	lung:	n/a	chr9:12814672-12814682 chr9:12814420-12814429
26	MXI1	chr9:12813653-12815194	IMR90	lung:	n/a	n/a
27	FOS	chr9:12814089-12815176	HUVEC	blood vessel:	n/a	chr9:12814448-12814460 chr9:12814593-12814603 chr9:12814594-12814603 chr9:12814593-12814602 chr9:12814501-12814510 chr9:12814597-12814605 chr9:12814592-12814603 chr9:12814594-12814601
28	POLR2A	chr9:12814109-12815287	HCT-116	colon:	n/a	n/a
29	MAX	chr9:12813973-12815094	HCT-116	colon:	n/a	chr9:12814672-12814682 chr9:12814420-12814429
30	EP300	chr9:12813339-12815175	Hela-S3	cervix:	n/a	chr9:12814418-12814432 chr9:12814594-12814603 chr9:12814543-12814557 chr9:12814499-12814508

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:12774109..12791345-chr9:12812800..12822770,37	MCF-7	breast:
2	chr9:12773974..12784053-chr9:12813051..12820453,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235448	TF binding region
ENSG00000153714	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10122949	0.83[EUR][1000 genomes]
rs10960800	0.84[EUR][1000 genomes]
rs10960803	0.88[EUR][1000 genomes]
rs10960804	0.88[EUR][1000 genomes]
rs10960805	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10960806	0.84[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10960807	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10960808	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10960812	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs10960813	0.90[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1318454	0.84[EUR][1000 genomes]
rs34919266	0.88[EUR][1000 genomes]
rs4397503	0.88[EUR][1000 genomes]
rs6474733	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6474736	0.90[CHD][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs71507332	0.84[EUR][1000 genomes]
rs7846724	0.87[CHD][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7859336	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9298684	0.92[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv892575	chr9:12804243-12852462	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12792000-12817200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:12808600-12818400	Weak transcription	Fetal Brain Male	brain
3	chr9:12809200-12817200	Weak transcription	Small Intestine	intestine
4	chr9:12809200-12821400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:12810400-12817600	Weak transcription	Gastric	stomach
6	chr9:12812200-12816200	Enhancers	Fetal Lung	lung
7	chr9:12812200-12816400	Weak transcription	Pancreas	Pancrea
8	chr9:12813400-12815200	Flanking Active TSS	HUVEC	blood vessel
9	chr9:12813600-12815200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:12813600-12816200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr9:12813800-12815200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr9:12813800-12815200	Enhancers	Fetal Stomach	stomach
13	chr9:12813800-12815600	Enhancers	Adipose Nuclei	Adipose
14	chr9:12814000-12815200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:12814000-12815200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:12814000-12815800	Enhancers	HSMM	muscle
17	chr9:12814200-12815200	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr9:12814400-12815200	Enhancers	Liver	Liver
19	chr9:12814400-12815200	Flanking Active TSS	Colon Smooth Muscle	Colon
20	chr9:12814400-12815400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:12814400-12815600	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr9:12814400-12816200	Enhancers	HSMMtube	muscle
23	chr9:12814400-12816800	Enhancers	NHDF-Ad	bronchial
24	chr9:12814400-12818800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:12814600-12815200	Enhancers	Brain Hippocampus Middle	brain
26	chr9:12814600-12815200	Enhancers	Stomach Mucosa	stomach
27	chr9:12814600-12815600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:12814600-12817400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:12814600-12817600	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr9:12814600-12819200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:12814600-12824800	Weak transcription	Psoas Muscle	Psoas
32	chr9:12814800-12815200	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr9:12814800-12815200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:12814800-12815200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:12814800-12815200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr9:12814800-12815200	Enhancers	Brain Anterior Caudate	brain
37	chr9:12814800-12815200	Flanking Active TSS	Fetal Intestine Large	intestine
38	chr9:12814800-12815200	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr9:12814800-12815200	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr9:12814800-12815200	Flanking Active TSS	A549	lung
41	chr9:12814800-12815200	Flanking Active TSS	Hela-S3	cervix
42	chr9:12814800-12815200	Flanking Active TSS	HMEC	breast
43	chr9:12814800-12815200	Flanking Active TSS	NH-A	brain
44	chr9:12814800-12815200	Flanking Active TSS	NHEK	skin
45	chr9:12814800-12815200	Flanking Active TSS	Osteobl	bone
46	chr9:12814800-12815400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:12814800-12817600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr9:12814800-12823200	Weak transcription	Colonic Mucosa	Colon
49	chr9:12815000-12815200	Enhancers	Brain Angular Gyrus	brain
50	chr9:12815000-12815200	Flanking Active TSS	NHLF	lung

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